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39 lines
1.5 KiB
Text
39 lines
1.5 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CMSEQ_POLYMUT } from '../../../../modules/cmseq/polymut/main.nf' addParams( options: [:] )
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workflow test_cmseq_polymut_1 {
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input_1 = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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[],
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file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
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[] ]
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CMSEQ_POLYMUT( input_1 )
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}
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workflow test_cmseq_polymut_2 {
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input_2 = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
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[] ]
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CMSEQ_POLYMUT( input_2 )
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}
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workflow test_cmseq_polymut_3 {
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input_3 = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), ]
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CMSEQ_POLYMUT( input_3 )
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}
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